Content Access Permissions Need To Be Rebuilt 6.14 to 6.16

I am in the process of upgrading a new clients site as both the core and quite a few modules were out of date. To do this as safely as possible, I duplicated the entire site and database on a dev server to go through the process there first. I began with the core update going from version 6.14 to 6.16. I followed all the instructions from backing everything up, disabling all add-on/non-core modules, to replacing existing files with the new ones, re-enabling the modules and running update.php. Everything seemed to go fine (ie: no error messages) with one exception. After re-enabling the previously disabled modules, the "The content access permissions need to be rebuilt. Please visit this page." message appeared. It appeared once before on the live site after a domain had been added and then removed via the Domain Access module. Not thinking it would be an issue to do as the message/link told me to do, I ran the script to Rebuild Permissions. The script hung multiple times, once I even let it run overnight. During that process anonymous users who are set to be able to view all content, were unable to access multiple content pages and menus disappeared as well. In the end we ended up reverting to a back-up of the site done a few days prior to the domain being added and removed. It was at that point that they finally agreed to let me go ahead with all of the recommended updates.

My question is two-fold.
First, as I am working on a copy of the live site, if I run the script to rebuild content access permissions, could it mess anything up since the domains stored in the Domain Access Module are for the live site?

Second, after my previous experience with this script, I am wary of having to run it again. While researching the problems we were having with running it, I ran across quite a few posts describing hanging issues. Were any changes made to this script in the newest version of Drupal I just upgraded to that go towards fixing the hanging problem? If not, is there anything I can do on my end prior to running the script that will help it to run as it is intended? This site has a ton of content/nodes and it was implied in one post I read that this makes the script take longer. I understand that, and that's fine, I just need it to work.

I look forward to and appreciate all responses. Thanks!